java.lang.Object
- org.scijava.ops.flim.FitParams

Type Parameters:

I - The type of the transient data.
```
public class FitParams>
extends Object
```
The collection of all fit parameters required to perform a single fit of an image. Fields named xxMap are image representations of the particular attribute. Other fields are not intended to be used by external programs and should be ignored when this object is processed with in the fitting ops.

Field Summary

Fields
Modifier and Type	Field	Description
`float`	`chisq_delta`	Stopping condition 2: stop if change in chi-squared is less than `chisq_target` (1E-4 by default)
`int`	`chisq_percent`	Confidence interval when calculating the error axes (95% by default)
`float`	`chisq_target`	Stopping condition 1: stop if reduced chi-squared is less than `chisq_target` (1 by default)
`boolean`	`dropBad`	Whether to declare `FitResults.retCode` as `FitResults.RET_BAD_FIT_CHISQ_OUT_OF_RANGE` or `FitResults.RET_BAD_FIT_DIVERGED` if `FitResults.chisq` is larger than 1e5 or less than 0.
`int`	`fitEnd`	The end of the decay interval
`flimlib.FitFunc`	`fitFunc`	The fitting model to use (Z + A_1e^(-t/tau_1) + A_2e^(-t/tau_2) + ...
`int`	`fitStart`	The start of the decay interval
`boolean`	`getChisqMap`	Whether to generate an image representation for chi-squred (`false` by default)
`boolean`	`getFittedMap`	Whether to generate an image representation for fitted transients (`false` by default)
`boolean`	`getParamMap`	Whether to generate an image representation for fitted parameters (`true` by default)
`boolean`	`getResidualsMap`	Whether to generate an image representation for residuals (`false` by default)
`boolean`	`getReturnCodeMap`	Whether to generate an image representation for the return codes (`false` by default)
`float[]`	`instr`	The array of instrument response (optional)
`float`	`iThresh`	Intensity threshold value (overrides `iThreshPercent`)
`float`	`iThreshPercent`	Intensity threshold percentage
`int`	`ltAxis`	The index of lifetime axis
`boolean`	`multithread`	Enable multithread fitting (`true` by default)
`int`	`nComp`	The number of exponential components of the fit (1 by default).
`flimlib.NoiseType`	`noise`	The assumed noise model of the fit (Poisson by default) @see NoiseType
`float[]`	`param`	The estimated parameters of the fit (global setting)
`boolean[]`	`paramFree`	The indicators of which of the parameters can be changed
`RandomAccessibleInterval<FloatType>`	`paramMap`	The image representation of the estimated parameters the fit (per-pixel setting, overides `param`)
`flimlib.RestrainType`	`restrain`	The fit restraint (`RestrainType.ECF_RESTRAIN_DEFAULT` by default)
`float[]`	`restraintMax`	The fit restraints (min or max) for each parameter.
`float[]`	`restraintMin`	The fit restraints (min or max) for each parameter.
`RealMask`	`roiMask`	The ROI mask (test() returns true on interested regions)
`float[]`	`sig`	The standard deviation (sigma) of the data, used for calculating chi-squared if `noise` is `NoiseType.NOISE_CONST` or `NoiseType.NOISE_GIVEN`.
`float[]`	`trans`	The transient data to fit
`RandomAccessibleInterval<I>`	`transMap`	The image representation of the dataset
`static int`	`UNINIT`	Fields with this value are uninitialized
`float`	`xInc`	The time increment between two consecutive data points

Constructor Summary

Constructors
Constructor Description

FitParams()

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`FitParams<I>`	`copy()`	Create a new instance of `FitParams` with shallow copy (maps are not duplicated).
`static <I extends RealType<I>> FitParams<I>`	`fromJSON(String jsonString)`	Creates a FitParams from serialized JSON string.
`String`	`toJSON()`	Serialize this FitParams into a JSON string.
`String`	`toString()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
 - UNINIT
```
@Expose
public static final int UNINIT
```
 Fields with this value are uninitialized
 
 See Also:
 
 Constant Field Values
 - xInc
```
@Expose
public float xInc
```
 The time increment between two consecutive data points
 - trans
```
public float[] trans
```
 The transient data to fit
 - ltAxis
```
@Expose
public int ltAxis
```
 The index of lifetime axis
 - transMap
```
public RandomAccessibleInterval> transMap
```
 The image representation of the dataset
 - roiMask
```
public RealMask roiMask
```
 The ROI mask (test() returns true on interested regions)
 - fitStart
```
@Expose
public int fitStart
```
 The start of the decay interval
 - fitEnd
```
@Expose
public int fitEnd
```
 The end of the decay interval
 - instr
```
@Expose
public float[] instr
```
 The array of instrument response (optional)
 - noise
```
@Expose
public flimlib.NoiseType noise
```
 The assumed noise model of the fit (Poisson by default) @see NoiseType
 - sig
```
@Expose
public float[] sig
```
 The standard deviation (sigma) of the data, used for calculating chi-squared if noise is NoiseType.NOISE_CONST or NoiseType.NOISE_GIVEN.
 - nComp
```
@Expose
public int nComp
```
 The number of exponential components of the fit (1 by default). This parameter is only used by LMA and Global ops, ignored otherwise.
 - param
```
@Expose
public float[] param
```
 The estimated parameters of the fit (global setting)
 - paramMap
```
public RandomAccessibleInterval<FloatType> paramMap
```
 The image representation of the estimated parameters the fit (per-pixel setting, overides param)
 - paramFree
```
@Expose
public boolean[] paramFree
```
 The indicators of which of the parameters can be changed
 - restrain
```
@Expose
public flimlib.RestrainType restrain
```
 The fit restraint (RestrainType.ECF_RESTRAIN_DEFAULT by default)
 - restraintMin
```
@Expose
public float[] restraintMin
```
 The fit restraints (min or max) for each parameter. A parameter at index i will be restrained during the fit in the range (restraintMin[i], restraintMax[i]). If any of the two bounds are not present (due to the array being null or [i] == NaN), then -/+Inf is used instead and that parameter will not be bounded from below/above. The bounds only take effect if restrain is set to RestrainType.ECF_RESTRAIN_USER.
 - restraintMax
```
@Expose
public float[] restraintMax
```
 The fit restraints (min or max) for each parameter. A parameter at index i will be restrained during the fit in the range (restraintMin[i], restraintMax[i]). If any of the two bounds are not present (due to the array being null or [i] == NaN), then -/+Inf is used instead and that parameter will not be bounded from below/above. The bounds only take effect if restrain is set to RestrainType.ECF_RESTRAIN_USER.
 - fitFunc
```
@Expose
public flimlib.FitFunc fitFunc
```
 The fitting model to use (Z + A_1e^(-t/tau_1) + A_2e^(-t/tau_2) + ... by default)
 - chisq_target
```
@Expose
public float chisq_target
```
 Stopping condition 1: stop if reduced chi-squared is less than chisq_target (1 by default)
 - chisq_delta
```
@Expose
public float chisq_delta
```
 Stopping condition 2: stop if change in chi-squared is less than chisq_target (1E-4 by default)
 - chisq_percent
```
@Expose
public int chisq_percent
```
 Confidence interval when calculating the error axes (95% by default)
 - iThresh
```
@Expose
public float iThresh
```
 Intensity threshold value (overrides iThreshPercent)
 - iThreshPercent
```
@Expose
public float iThreshPercent
```
 Intensity threshold percentage
 - multithread
```
@Expose
public boolean multithread
```
 Enable multithread fitting (true by default)
 - dropBad
```
@Expose
public boolean dropBad
```
 Whether to declare FitResults.retCode as FitResults.RET_BAD_FIT_CHISQ_OUT_OF_RANGE or FitResults.RET_BAD_FIT_DIVERGED if FitResults.chisq is larger than 1e5 or less than 0.
 - getReturnCodeMap
```
@Expose
public boolean getReturnCodeMap
```
 Whether to generate an image representation for the return codes (false by default)
 - getParamMap
```
@Expose
public boolean getParamMap
```
 Whether to generate an image representation for fitted parameters (true by default)
 - getFittedMap
```
@Expose
public boolean getFittedMap
```
 Whether to generate an image representation for fitted transients (false by default)
 - getResidualsMap
```
@Expose
public boolean getResidualsMap
```
 Whether to generate an image representation for residuals (false by default)
 - getChisqMap
```
@Expose
public boolean getChisqMap
```
 Whether to generate an image representation for chi-squred (false by default)
- Constructor Detail
 - FitParams
```
public FitParams()
```
- Method Detail
 - copy
```
public FitParams copy()
```
 Create a new instance of FitParams with shallow copy (maps are not duplicated).
 
 Returns:
 
 A clone of the current instance.
 - toJSON
```
public String toJSON()
```
 Serialize this FitParams into a JSON string. trans, transMap, roiMask, and paramMap are skipped.
 
 Returns:
 
 the JSON string
 - fromJSON
```
public static > FitParams fromJSON(String jsonString)
```
 Creates a FitParams from serialized JSON string.
 
 Type Parameters:
 
 I - data type
 
 Parameters:
 
 jsonString - the JSON string produced by toJSON()
 
 Returns:
 
 the serialized parameters
 - toString
```
public String toString()
```
 Overrides:
 
 toString in class Object

Class FitParams<I extends RealType<I>>

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

UNINIT

xInc

trans

ltAxis

transMap

roiMask

fitStart

fitEnd

instr

noise

sig

nComp

param

paramMap

paramFree

restrain

restraintMin

restraintMax

fitFunc

chisq_target

chisq_delta

chisq_percent

iThresh

iThreshPercent

multithread

dropBad

getReturnCodeMap

getParamMap

getFittedMap

getResidualsMap

getChisqMap

Constructor Detail

FitParams

Method Detail

copy

toJSON

fromJSON

toString